Climate change has been revealed to increase the occurrence of natural disasters and to damage ecological systems. In coastal regions, there are many environmentally significant areas from the viewpoint of biodiversity, such as areas registered under the Ramsar Convention. The Kushiro Wetland is the largest wetland and one of the most significant natural systems in Japan, remaining mostly unaffected by human activity. In the wetland, there are many species, which do not tolerate saltwater. When the sea level rises, the communities of freshwater plants and fish may die out due to the extension of salt wedge intrusion along the Kushiro River. Therefore, in this study we make an attempt to understand the impact of sea level rise on the ecological system of the wetland by using a three-dimensional numerical model, which allows us to evaluate the effect of sea level rise on salt wedge intrusion. It is revealed that the National Park area may be affected by salt water when sea level rise reaches about 0.15 m. Also, the maximum sea level rise may induce saltwater intrusion into the Ramsar area. As a result, we proposed an adaptive management strategy for protecting the ecological system of the wetland from salt wedge intrusion.